Researchers at RIKEN, Japan’s flagship research organization, have developed a
ground-breaking new aqueous reagent which literally turns biological tissue
transparent. Experiments using fluorescence microscopy on samples treated
with the reagent, published this week in Nature Neuroscience, have produced
vivid 3D images of neurons and blood vessels deep inside the mouse brain.
Highly effective and cheap to produce, the reagent offers an ideal means for
analyzing the complex organs and networks that sustain living systems.

Our understanding of biological organisms and
how they function is intrinsically tied to the limits
of what we can actually see. Even today’s most
promising techniques for visualizing biological
tissue face this limitation: mechanical methods
require that samples be sectioned into smaller
pieces for visualization, while optical methods
are prevented by the scattering property of light
from probing deeper than 1mm into tissue.
Either way, the full scope and detail of the
biological sample is lost.

The new reagent, referred to as Scale and developed by Atsushi Miyawaki and his team
at the RIKEN Brain Science Institute (BSI), gets around these problems by doing two
things together that no earlier technique has managed to do. The first is to render
biological tissue transparent. Scale does this significantly better than other clearing
reagents and without altering the overall shape or proportions of the sample. The
second is to avoid decreasing the intensity of signals emitted by genetically-encoded
fluorescent proteins in the tissue, which are used as markers to label specific cell types.

This combination makes possible a revolution in optical imaging, enabling researchers
to visualize fluorescently-labeled brain samples at a depth of several millimeters and
reconstruct neural networks at sub-cellular resolution. Already, Miyawaki and his team
have used Scale to study neurons in the mouse brain at an unprecedented depth and
level of resolution, shedding light onto the intricate networks of the cerebral cortex,
hippocampus and white matter. Initial experiments exploit Scale’s unique properties to
visualize the axons connecting left and right hemispheres and blood vessels in the
postnatal hippocampus in greater detail than ever before.

But the potential of Scale goes much further. “Our current experiments are focused on
the mouse brain, but applications are neither limited to mice, nor to the brain,” Miyawaki
explains. “We envision using Scale on other organs such as the heart, muscles and
kidneys, and on tissues from primate and human biopsy samples.”

Looking ahead, Miyawaki’s team has set its sights on an ambitious goal. “We are
currently investigating another, milder candidate reagent which would allow us to study
live tissue in the same way, at somewhat lower levels of transparency. This would open
the door to experiments that have simply never been possible before.”

RIKEN is Japan’s flagship research institute devoted to basic and applied research.
Over 2500 papers by RIKEN researchers are published every year in reputable
scientific and technical journals, covering topics ranging across a broad spectrum of
disciplines including physics, chemistry, biology, medical science and engineering.
RIKEN’s advanced research environment and strong emphasis on interdisciplinary
collaboration has earned itself an unparalleled reputation for scientific excellence in
Japan and around the world.

About the RIKEN Brain Science Institute

The RIKEN Brain Science Institute (BSI) was established as an institute at RIKEN in
October, 1997 to answer a growing need in society for cutting-edge brain science
research. Since its establishment, BSI has attracted promising scientists domestically
and internationally and brought together diverse research and human resources, and
today enjoys an international reputation as an innovative center for brain science.